Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Papio anubis Transcriptome or Gene expression

ABSTRACT: This data set consists of tissue-specific RNA-seq reads from 14 different tissues from a single female adult olive baboon (Papio anubis): bone marrow, brain cerebellum, brain frontal cortex, brain pituitary, brain temporal lobe, colon, heart, kidney, liver, lymph node, spleen, lung, skeletal muscle and thymus. The data set was generated by the non-human primate reference transcriptome resource (NHPRTR) project (http://nhprtr.org/), and was first made public on 14 Jan 2014.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Papio anubis

SUBMITTER: Michael Katze

PROVIDER: E-MTAB-2848 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics.

Pipes Lenore L Li Sheng S Bozinoski Marjan M Palermo Robert R Peng Xinxia X Blood Phillip P Kelly Sara S Weiss Jeffrey M JM Thierry-Mieg Jean J Thierry-Mieg Danielle D Zumbo Paul P Chen Ronghua R Schroth Gary P GP Mason Christopher E CE Katze Michael G MG

Nucleic acids research 20121129 Database issue

RNA-based next-generation sequencing (RNA-Seq) provides a tremendous amount of new information regarding gene and transcript structure, expression and regulation. This is particularly true for non-coding RNAs where whole transcriptome analyses have revealed that the much of the genome is transcribed and that many non-coding transcripts have widespread functionality. However, uniform resources for raw, cleaned and processed RNA-Seq data are sparse for most organisms and this is especially true fo ...[more]

PMID: 23203872

Similar Datasets

Parent of origin allelic expression bias in mouse vomernasal organ

Project description:An allele of a gene can be epigenetically regulated to show a parent-of-origin biasedexpression pattern, a phenomenon referring to as genomic imprinting. Genomic imprinting ishighly tissue-specific, and mammalian brains are hotspots for this effect. Social behaviourdefects in human and various behavioural changes in mouse, had been linked toinappropriate imprinting, but little is known about how and why such effects occur.The olfactory system in the brain is the essential sensory circuitry that mediates rodent innatebehaviour. Meanwhile, monoallelic expression, a related process, is used extensively inchemosensory neurons to regulate olfactory and vomeronasal receptor choice. We have datashowing receptor gene choice is not a random process, which implies allele choice may bebiased also. The olfactory system is therefore a promising target for detecting allelicimbalance, or even novel imprinting genes, by high-resolution RNA-sequencing followed byallelic-specific transcriptomic mapping.This project is designed to detect parent-of-origin and strain-of-origin allelic expression bias inneurons from a key olfactory tissues in rodents: vomernasal organ (VNO) . RNA from reciprocally crossed F1 hybrid mice (S-cross and M-cross) from two distinct inbred strains (C57BL/6J and CAST) have been extracted respectively. After sequencing,expression levels from each allele will be distinguished by incorporating SNP and indeldifferences to the strain-specific reference genomes. Analysis will be carried out incollaboration with Gary Churchill's team at the Jackson Laboratory (who have developed amethod of analysing RNAseq data from CAST x C57BL/6J F1s).Genes with strong, reproducible allelic imbalances will be followed up to assess the functional consequences.

2014-12-09 | E-ERAD-318 | biostudies-arrayexpress

Detecting parent of origin allelic expression bias in mouse olfaction system

Project description:An allele of a gene can be epigenetically regulated to show a parent-of-origin biasedexpression pattern, a phenomenon referring to as genomic imprinting. Genomic imprinting ishighly tissue-specific, and mammalian brains are hotspots for this effect. Social behaviourdefects in human and various behavioural changes in mouse, had been linked toinappropriate imprinting, but little is known about how and why such effects occur.The olfactory system in the brain is the essential sensory circuitry that mediates rodent innatebehaviour. Meanwhile, monoallelic expression, a related process, is used extensively inchemosensory neurons to regulate olfactory and vomeronasal receptor choice. We have datashowing receptor gene choice is not a random process, which implies allele choice may bebiased also. The olfactory system is therefore a promising target for detecting allelicimbalance, or even novel imprinting genes, by high-resolution RNA-sequencing followed byallelic-specific transcriptomic mapping.This project is designed to detect parent-of-origin and strain-of-origin allelic expression bias inneurons from two olfactory tissues: main olfactory epithelium (MOE) and olfaction bulb (OB). RNA from reciprocally crossed F1 hybrid mice (S-cross and M-cross) from two distinct inbred strains (C57BL/6J and CAST) have been extracted respectively (two crosses, two tissue types). After sequencing,expression levels from each allele will be distinguished by incorporating SNP and indeldifferences to the strain-specific reference genomes. Analysis will be carried out incollaboration with Gary Churchill's team at the Jackson Laboratory (who have developed amethod of analysing RNAseq data from CAST x C57BL/6J F1s).Genes with strong, reproducible allelic imbalances will be followed up to assess the functional consequences.

2014-05-27 | E-ERAD-239 | biostudies-arrayexpress

MICROME single carbon source testing by TraDIS

Project description:http://www.sanger.ac.uk/resources/downloads/bacteria/salmonella.html

2013-06-26 | E-ERAD-5 | biostudies-arrayexpress

TTV018 RORC IBD associated genotype effects on RORgT expression and function in ex vivo T cells

Project description:RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-07-11 | E-ERAD-443 | biostudies-arrayexpress

Study of low dose gamma irradiation effects in esophageal epithelial cell fate

Project description:Effect of low-doses of ionizing radiation on the behaviour of epithelial cells. The aim of the study is to check whether a single exposure of 50 mGy of ioninzing radiation promotes changes in RNA transcription levels and/or mutations.

2016-02-23 | E-ERAD-429 | biostudies-arrayexpress

Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition.

Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.

2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress

Oryza sativa strain:Nipponbare Transcriptome or Gene expression

Project description: Not available

2014-11-04 | E-MTAB-4123 | biostudies-arrayexpress

Populus trichocarpa Transcriptome or Gene expression

Project description:Our analysis provides a comprehensive picture of how P. trichocarpa responds to drought stress at physiological and transcriptome levels which may help to understand molecular mechanisms associated with drought response and could be useful for genetic engineering of woody plants. Drought stress treatment was performed dividing P. trichocarpa plants into the well-watered (WW) group (soil volumetric water content of 40â45 %) and the water-limited group (soil volumetric water content of 10â15 %). Two cDNA libraries constructed separately from the WW and WL groups were subjected to high-throughput Illumina sequencing.

2013-11-20 | E-MTAB-4126 | biostudies-arrayexpress

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4 Kranz anatomy

Project description:Photosynthesis underpins the viability of most ecosystems, with C4 plants that exhibit âKranzâ anatomy being the most efficient primary producers. Kranz anatomy is characterized by closely spaced veins that are encircled by two morphologically distinct photosynthetic cell types. Although Kranz anatomy evolved multiple times, the underlying genetic mechanisms remain largely elusive, with only the maize scarecrow gene so far implicated in Kranz patterning. To provide a broader insight into the regulation of Kranz differentiation, we performed a genome-wide comparative analysis of developmental trajectories in Kranz (foliar leaf blade) and non-Kranz (husk leaf sheath) leaves of the C4 plant maize. Using profile classification of gene expression in early leaf primordia, we identified cohorts of genes associated with procambium initiation and vascular patterning. In addition, we used supervised classification criteria inferred from anatomical and developmental analyses of five developmental stages to identify candidate regulators of cell-type specification. Our analysis supports the suggestion that Kranz anatomy is patterned, at least in part, by a SCARECROW/SHORTROOT regulatory network, and suggests likely components of that network. Furthermore, the data imply a role for additional pathways in the development of Kranz leaves.

2013-07-29 | E-MTAB-4134 | biostudies-arrayexpress

Zea mays Transcriptome or Gene expression

Project description:The classical maize mutant lazy1 (la1), displayed prostrate growth with reduced shoot gravitropism. We compared the transcriptome profile of the third node in la1-ref mutants with those in wild-type plants using RNA-SEQ to examine the genome-wide effect of the ZmLA1 gene. We generated 14.6 and 36.5 million paired-end reads from two biological samples of wild-type and la1-ref mutant plants, respectively.

2013-11-20 | E-MTAB-4196 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data